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934
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934 results for “Amino acids”
Relative roles of Stp1 and Stp2 in amino acid and peptide utilization in Candida albicans
GEO Series GSE145576. Candida albicans SC5314. 27 samples. Type: Expression profiling by high throughput sequencing.
Short-Term Time-Restricted Feeding Alters Rhythmicity of Lipid and Amino Acid Metabolites in Overweight Men
GEO Series GSE129843. Homo sapiens. 125 samples. Type: Expression profiling by high throughput sequencing.
Amino acid stress response genes promote L-asparaginase resistance in pediatric acute lymphoblastic leukemia [RNA-seq]
GEO Series GSE174498. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing.
The role of GCN2 kinase in amino acid dependent longevity and feeding behaviour in Drosophila
GEO Series GSE203210. Drosophila melanogaster. 24 samples. Type: Expression profiling by high throughput sequencing.
Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
GEO Series GSE291653. Mus musculus. 18 samples. Type: Other.
Activation of YAP/TAZ signaling reprograms the airway secretory cell fate via mTORC1-dependent amino acid metabolism
GEO Series GSE178829. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Distinct effects of restricting individual branched-chain amino acids on the development and progression of Alzheimer’s disease in 3xTg mice
GEO Series GSE299928. Mus musculus. 47 samples. Type: Expression profiling by high throughput sequencing.
GCGR Loss-of-Function Mutations Promote Amino Acid-Dependent Pancreatic Neuroendocrine Tumor Initiation from a Subpopulation of Alpha Cells [single-cell RNA-seq]
GEO Series GSE142233. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
TimeLapse-seq after amino acid starvation in Mettl3 knockout MEF
GEO Series GSE249256. Mus musculus. 12 samples. Type: Other.
Tree and amino acid alignments of thioredoxin, glucose-6-phosphate dehydrogenase, and malate dehydrogenase
<p>Redox regulation in phytoplankton is critical to monitor and stabilize metabolic pathways under changing environmental conditions. In plastids, the thioredoxin (TRX) system is linked to photosynthetic electron transport and fine tuning the metabolism to fluctuating light levels. Expansion of the number of redox signal transmitters and their protein targets, as seen in plants, is believed to increase cell robustness. In this study, we searched for genes related to redox regulation in the genome of the photosynthetic amoeba <i>Paulinella micropora </i>KR01 (hereafter, KR01). The genus <i>Paulinella </i>includes testate filose amoebae, in which a single clade acquired a photosynthetic organelle, the chromatophore, from an alpha cyanobacterial donor<i>. </i>This independent primary endosymbiosis occurred relatively recently (~ 124 Ma), when compared to Archaeplastida (> 1 Ga), making photosynthetic <i>Paulinella </i>a valuable model for studying the earlier stages of primary endosymbiosis.<i> </i>Our comparative analysis demonstrates that this lineage has<i> </i>evolved a thioredoxin system similar to that from other algae, relying however on genes with diverse phylogenetic origins (i.e., the endosymbiont, host, bacteria, red algae). One TRX of eukaryotic provenance is targeted to the chromatophore, implicating host-endosymbiont coordination of redox regulation. A chromatophore targeted glucose-6-phosphate dehydrogenase of red algal origin suggests that <i>Paulinella </i>exploited the existing redox regulation system in Archaeplastida to foster integration. Our study elucidates the independent evolution of the thioredoxin system in photosynthetic <i>Paulinella</i>, whose parts derive from the existing genetic toolkit in diverse organisms.</p>
Data from: Coevolution-based inference of amino acid interactions underlying protein function
Protein function arises from a poorly understood pattern of energetic interactions between amino acid residues. Sequence-based strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here, we extend deep-mutation technologies to enable measurement of many thousands of pairwise amino acid couplings in several homologs of a protein family – a deep coupling scan (DCS). The data show that cooperative interactions between residues are loaded in a sparse, evolutionarily conserved, spatially contiguous network of amino acids. The pattern of amino acid coupling is quantitatively captured in the coevolution of amino acid positions, especially as indicated by the statistical coupling analysis (SCA), providing experimental confirmation of the key tenets of this method. This work exposes the collective nature of physical constraints on protein function and clarifies its link with sequence analysis, enabling a general practical approach for understanding the structural basis for protein function.
Supplements for "The Proteomic Code: Novel Amino Acid Residue Pairing Models "Encode" Protein Folding and Protein-Protein Interactions"
<p><strong>Supplements for "The Proteomic Code: Novel Amino Acid Residue Pairing Models “Encode” Protein Folding and Protein-Protein Interactions"</strong></p> <p>This supplement includes the following files:</p> <ul> <li>Main_v02.R --- Script in R language to process protein structures and produce the datasets.</li> <li>datasets_v02.zip --- final filtered version of datasets produced in R language (by "Main_v02.R"). </li> <li>Dataset key v02.txt --- key and descriptions to column names in ("datasets.zip"). </li> </ul> <p>The article featuring these datasets is submitted to:</p> <p>Journal: Computers in Biology and Medicine (Reference: CBM_110033)<br>Title: "The Proteomic Code: Novel Amino Acid Residue Pairing Models "Encode" Protein Folding and Protein-Protein Interactions"<br>Authors: Hameduh, Tareq; Miller, Andrew D. ; Heger, Zbynek; Haddad, Yazan</p> <p> </p> <p> </p>
Figure 2 from: Slobodianiuk L, Budniak L, Marchyshyn S, Kostyshyn L, Ezhned M (2021) Determination of amino acids content of the Tagetes lucida Cav. by GC/MS. Pharmacia 68(4): 859-867. https://doi.org/10.3897/pharmacia.68.e73325
Figure 2 GC/MS chromatogram of bound amino acids of Tagetes lucida herb.
Figure 3 from: Slobodianiuk L, Budniak L, Marchyshyn S, Kostyshyn L, Ezhned M (2021) Determination of amino acids content of the Tagetes lucida Cav. by GC/MS. Pharmacia 68(4): 859-867. https://doi.org/10.3897/pharmacia.68.e73325
Figure 3 GC/MS chromatogram of free amino acids of Tagetes lucida flowers.
Figure 6 from: Slobodianiuk L, Budniak L, Marchyshyn S, Kostyshyn L, Ezhned M (2021) Determination of amino acids content of the Tagetes lucida Cav. by GC/MS. Pharmacia 68(4): 859-867. https://doi.org/10.3897/pharmacia.68.e73325
Figure 6 GC/MS chromatogram of bound amino acids of Tagetes lucida leaves.
Figure 5 from: Slobodianiuk L, Budniak L, Marchyshyn S, Kostyshyn L, Ezhned M (2021) Determination of amino acids content of the Tagetes lucida Cav. by GC/MS. Pharmacia 68(4): 859-867. https://doi.org/10.3897/pharmacia.68.e73325
Figure 5 GC/MS chromatogram of free amino acids of Tagetes lucida leaves.
Figure 4 from: Slobodianiuk L, Budniak L, Marchyshyn S, Kostyshyn L, Ezhned M (2021) Determination of amino acids content of the Tagetes lucida Cav. by GC/MS. Pharmacia 68(4): 859-867. https://doi.org/10.3897/pharmacia.68.e73325
Figure 4 GC/MS chromatogram of bound amino acids of Tagetes lucida flowers.
Figure 1 from: Slobodianiuk L, Budniak L, Marchyshyn S, Kostyshyn L, Ezhned M (2021) Determination of amino acids content of the Tagetes lucida Cav. by GC/MS. Pharmacia 68(4): 859-867. https://doi.org/10.3897/pharmacia.68.e73325
Figure 1 GC/MS chromatogram of free amino acids of Tagetes lucida herb.
Figure 8 from: Savych A, Marchyshyn S, Mosula L, Bilyk O, Humeniuk I, Davidenko A (2022) Analysis of amino acids content in the plant components of the antidiabetic herbal mixture by GC-MS. Pharmacia 69(1): 69-76. https://doi.org/10.3897/pharmacia.69.e77251
Figure 8 GC-MS chromatogram of derivatives of amino acids after hydrolysis in Taraxaci radices.
Figure 5 from: Savych A, Marchyshyn S, Mosula L, Bilyk O, Humeniuk I, Davidenko A (2022) Analysis of amino acids content in the plant components of the antidiabetic herbal mixture by GC-MS. Pharmacia 69(1): 69-76. https://doi.org/10.3897/pharmacia.69.e77251
Figure 5 GC-MS chromatogram of derivatives of free amino acids in Rosae fructus.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.